vcf_clone_detect.py results for M. capitata RNA-seq samples from this study and SRASetup R env. Load packages and set default image export formats, size and resolution.
knitr::opts_chunk$set(echo = TRUE,
fig.height = 12,
fig.width = 12,
dev = c("png", "pdf"),
dpi = 1000)
library(readxl)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(ggplot2)
library(gplots)
##
## Attaching package: 'gplots'
## The following object is masked from 'package:stats':
##
## lowess
library(reshape2)
library(RcppCNPy)
library(tibble)
library(ggdendro)
library(cowplot)
library(RColorBrewer)
library(viridis)
## Loading required package: viridisLite
library(knitr)
library(plotly)
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
library(phylogram)
options(scipen = 999) #Prevent scientific notation
cexSize <- 0.3
Load file with annotation for each sample.
samples.info <- read.table("../../../samples_Mcapitata_ALL.annotations.txt", header=T, comment.char='')
rownames(samples.info) <- samples.info$sample
samples.info
## sample species
## Mcapitata_ATAC_TP11_2302 Mcapitata_ATAC_TP11_2302 Mcapitata
## Mcapitata_HTAC_TP11_2380 Mcapitata_HTAC_TP11_2380 Mcapitata
## Mcapitata_ATAC_TP6_2402 Mcapitata_ATAC_TP6_2402 Mcapitata
## Mcapitata_ATAC_TP12_2403 Mcapitata_ATAC_TP12_2403 Mcapitata
## Mcapitata_ATAC_TP1_1037 Mcapitata_ATAC_TP1_1037 Mcapitata
## Mcapitata_ATAC_TP1_1600 Mcapitata_ATAC_TP1_1600 Mcapitata
## Mcapitata_ATAC_TP1_1652 Mcapitata_ATAC_TP1_1652 Mcapitata
## Mcapitata_ATAC_TP3_1101 Mcapitata_ATAC_TP3_1101 Mcapitata
## Mcapitata_ATAC_TP3_1548 Mcapitata_ATAC_TP3_1548 Mcapitata
## Mcapitata_ATAC_TP3_1628 Mcapitata_ATAC_TP3_1628 Mcapitata
## Mcapitata_ATAC_TP4_1108 Mcapitata_ATAC_TP4_1108 Mcapitata
## Mcapitata_ATAC_TP4_1609 Mcapitata_ATAC_TP4_1609 Mcapitata
## Mcapitata_ATAC_TP4_1651 Mcapitata_ATAC_TP4_1651 Mcapitata
## Mcapitata_ATAC_TP5_1196 Mcapitata_ATAC_TP5_1196 Mcapitata
## Mcapitata_ATAC_TP5_1610 Mcapitata_ATAC_TP5_1610 Mcapitata
## Mcapitata_ATAC_TP5_1776 Mcapitata_ATAC_TP5_1776 Mcapitata
## Mcapitata_ATAC_TP6_1114 Mcapitata_ATAC_TP6_1114 Mcapitata
## Mcapitata_ATAC_TP6_1611 Mcapitata_ATAC_TP6_1611 Mcapitata
## Mcapitata_ATAC_TP7_1058 Mcapitata_ATAC_TP7_1058 Mcapitata
## Mcapitata_ATAC_TP7_1455 Mcapitata_ATAC_TP7_1455 Mcapitata
## Mcapitata_ATAC_TP7_1499 Mcapitata_ATAC_TP7_1499 Mcapitata
## Mcapitata_ATAC_TP8_1083 Mcapitata_ATAC_TP8_1083 Mcapitata
## Mcapitata_ATAC_TP8_1436 Mcapitata_ATAC_TP8_1436 Mcapitata
## Mcapitata_ATAC_TP8_1779 Mcapitata_ATAC_TP8_1779 Mcapitata
## Mcapitata_ATAC_TP9_1121 Mcapitata_ATAC_TP9_1121 Mcapitata
## Mcapitata_ATAC_TP9_1420 Mcapitata_ATAC_TP9_1420 Mcapitata
## Mcapitata_ATAC_TP9_1580 Mcapitata_ATAC_TP9_1580 Mcapitata
## Mcapitata_ATAC_TP10_1095 Mcapitata_ATAC_TP10_1095 Mcapitata
## Mcapitata_ATAC_TP10_1561 Mcapitata_ATAC_TP10_1561 Mcapitata
## Mcapitata_ATAC_TP10_1631 Mcapitata_ATAC_TP10_1631 Mcapitata
## Mcapitata_ATAC_TP11_1076 Mcapitata_ATAC_TP11_1076 Mcapitata
## Mcapitata_ATAC_TP11_1644 Mcapitata_ATAC_TP11_1644 Mcapitata
## Mcapitata_ATAC_TP12_1120 Mcapitata_ATAC_TP12_1120 Mcapitata
## Mcapitata_ATAC_TP12_1452 Mcapitata_ATAC_TP12_1452 Mcapitata
## Mcapitata_ATHC_TP1_1218 Mcapitata_ATHC_TP1_1218 Mcapitata
## Mcapitata_ATHC_TP1_1826 Mcapitata_ATHC_TP1_1826 Mcapitata
## Mcapitata_ATHC_TP1_2068 Mcapitata_ATHC_TP1_2068 Mcapitata
## Mcapitata_ATHC_TP3_1544 Mcapitata_ATHC_TP3_1544 Mcapitata
## Mcapitata_ATHC_TP3_2731 Mcapitata_ATHC_TP3_2731 Mcapitata
## Mcapitata_ATHC_TP3_2866 Mcapitata_ATHC_TP3_2866 Mcapitata
## Mcapitata_ATHC_TP4_1221 Mcapitata_ATHC_TP4_1221 Mcapitata
## Mcapitata_ATHC_TP4_2561 Mcapitata_ATHC_TP4_2561 Mcapitata
## Mcapitata_ATHC_TP4_2734 Mcapitata_ATHC_TP4_2734 Mcapitata
## Mcapitata_ATHC_TP5_1229 Mcapitata_ATHC_TP5_1229 Mcapitata
## Mcapitata_ATHC_TP5_1706 Mcapitata_ATHC_TP5_1706 Mcapitata
## Mcapitata_ATHC_TP5_2986 Mcapitata_ATHC_TP5_2986 Mcapitata
## Mcapitata_ATHC_TP6_1212 Mcapitata_ATHC_TP6_1212 Mcapitata
## Mcapitata_ATHC_TP6_2016 Mcapitata_ATHC_TP6_2016 Mcapitata
## Mcapitata_ATHC_TP6_2555 Mcapitata_ATHC_TP6_2555 Mcapitata
## Mcapitata_ATHC_TP7_1223 Mcapitata_ATHC_TP7_1223 Mcapitata
## Mcapitata_ATHC_TP7_2860 Mcapitata_ATHC_TP7_2860 Mcapitata
## Mcapitata_ATHC_TP7_2875 Mcapitata_ATHC_TP7_2875 Mcapitata
## Mcapitata_ATHC_TP8_1260 Mcapitata_ATHC_TP8_1260 Mcapitata
## Mcapitata_ATHC_TP8_2735 Mcapitata_ATHC_TP8_2735 Mcapitata
## Mcapitata_ATHC_TP8_2753 Mcapitata_ATHC_TP8_2753 Mcapitata
## Mcapitata_ATHC_TP9_1148 Mcapitata_ATHC_TP9_1148 Mcapitata
## Mcapitata_ATHC_TP9_2862 Mcapitata_ATHC_TP9_2862 Mcapitata
## Mcapitata_ATHC_TP9_2995 Mcapitata_ATHC_TP9_2995 Mcapitata
## Mcapitata_ATHC_TP10_1204 Mcapitata_ATHC_TP10_1204 Mcapitata
## Mcapitata_ATHC_TP10_2554 Mcapitata_ATHC_TP10_2554 Mcapitata
## Mcapitata_ATHC_TP10_2737 Mcapitata_ATHC_TP10_2737 Mcapitata
## Mcapitata_ATHC_TP11_1237 Mcapitata_ATHC_TP11_1237 Mcapitata
## Mcapitata_ATHC_TP11_2188 Mcapitata_ATHC_TP11_2188 Mcapitata
## Mcapitata_ATHC_TP11_2756 Mcapitata_ATHC_TP11_2756 Mcapitata
## Mcapitata_ATHC_TP12_1154 Mcapitata_ATHC_TP12_1154 Mcapitata
## Mcapitata_ATHC_TP12_2736 Mcapitata_ATHC_TP12_2736 Mcapitata
## Mcapitata_ATHC_TP12_2990 Mcapitata_ATHC_TP12_2990 Mcapitata
## Mcapitata_HTAC_TP1_1579 Mcapitata_HTAC_TP1_1579 Mcapitata
## Mcapitata_HTAC_TP1_2153 Mcapitata_HTAC_TP1_2153 Mcapitata
## Mcapitata_HTAC_TP1_2183 Mcapitata_HTAC_TP1_2183 Mcapitata
## Mcapitata_HTAC_TP3_1289 Mcapitata_HTAC_TP3_1289 Mcapitata
## Mcapitata_HTAC_TP3_1751 Mcapitata_HTAC_TP3_1751 Mcapitata
## Mcapitata_HTAC_TP3_2021 Mcapitata_HTAC_TP3_2021 Mcapitata
## Mcapitata_HTAC_TP4_1269 Mcapitata_HTAC_TP4_1269 Mcapitata
## Mcapitata_HTAC_TP4_1481 Mcapitata_HTAC_TP4_1481 Mcapitata
## Mcapitata_HTAC_TP4_2000 Mcapitata_HTAC_TP4_2000 Mcapitata
## Mcapitata_HTAC_TP5_1321 Mcapitata_HTAC_TP5_1321 Mcapitata
## Mcapitata_HTAC_TP5_1583 Mcapitata_HTAC_TP5_1583 Mcapitata
## Mcapitata_HTAC_TP5_1997 Mcapitata_HTAC_TP5_1997 Mcapitata
## Mcapitata_HTAC_TP6_1496 Mcapitata_HTAC_TP6_1496 Mcapitata
## Mcapitata_HTAC_TP6_1588 Mcapitata_HTAC_TP6_1588 Mcapitata
## Mcapitata_HTAC_TP6_1705 Mcapitata_HTAC_TP6_1705 Mcapitata
## Mcapitata_HTAC_TP7_1278 Mcapitata_HTAC_TP7_1278 Mcapitata
## Mcapitata_HTAC_TP7_1645 Mcapitata_HTAC_TP7_1645 Mcapitata
## Mcapitata_HTAC_TP7_1722 Mcapitata_HTAC_TP7_1722 Mcapitata
## Mcapitata_HTAC_TP8_1235 Mcapitata_HTAC_TP8_1235 Mcapitata
## Mcapitata_HTAC_TP8_2386 Mcapitata_HTAC_TP8_2386 Mcapitata
## Mcapitata_HTAC_TP8_2410 Mcapitata_HTAC_TP8_2410 Mcapitata
## Mcapitata_HTAC_TP9_1306 Mcapitata_HTAC_TP9_1306 Mcapitata
## Mcapitata_HTAC_TP9_1467 Mcapitata_HTAC_TP9_1467 Mcapitata
## Mcapitata_HTAC_TP9_2412 Mcapitata_HTAC_TP9_2412 Mcapitata
## Mcapitata_HTAC_TP10_1315 Mcapitata_HTAC_TP10_1315 Mcapitata
## Mcapitata_HTAC_TP10_1478 Mcapitata_HTAC_TP10_1478 Mcapitata
## Mcapitata_HTAC_TP10_1754 Mcapitata_HTAC_TP10_1754 Mcapitata
## Mcapitata_HTAC_TP11_1248 Mcapitata_HTAC_TP11_1248 Mcapitata
## Mcapitata_HTAC_TP11_1562 Mcapitata_HTAC_TP11_1562 Mcapitata
## Mcapitata_HTAC_TP12_1632 Mcapitata_HTAC_TP12_1632 Mcapitata
## Mcapitata_HTAC_TP12_1729 Mcapitata_HTAC_TP12_1729 Mcapitata
## Mcapitata_HTAC_TP12_2007 Mcapitata_HTAC_TP12_2007 Mcapitata
## Mcapitata_HTHC_TP1_1145 Mcapitata_HTHC_TP1_1145 Mcapitata
## Mcapitata_HTHC_TP1_1323 Mcapitata_HTHC_TP1_1323 Mcapitata
## Mcapitata_HTHC_TP1_2081 Mcapitata_HTHC_TP1_2081 Mcapitata
## Mcapitata_HTHC_TP3_1128 Mcapitata_HTHC_TP3_1128 Mcapitata
## Mcapitata_HTHC_TP3_1277 Mcapitata_HTHC_TP3_1277 Mcapitata
## Mcapitata_HTHC_TP3_2518 Mcapitata_HTHC_TP3_2518 Mcapitata
## Mcapitata_HTHC_TP4_1124 Mcapitata_HTHC_TP4_1124 Mcapitata
## Mcapitata_HTHC_TP4_1328 Mcapitata_HTHC_TP4_1328 Mcapitata
## Mcapitata_HTHC_TP4_2204 Mcapitata_HTHC_TP4_2204 Mcapitata
## Mcapitata_HTHC_TP5_1345 Mcapitata_HTHC_TP5_1345 Mcapitata
## Mcapitata_HTHC_TP5_1449 Mcapitata_HTHC_TP5_1449 Mcapitata
## Mcapitata_HTHC_TP5_1694 Mcapitata_HTHC_TP5_1694 Mcapitata
## Mcapitata_HTHC_TP6_1164 Mcapitata_HTHC_TP6_1164 Mcapitata
## Mcapitata_HTHC_TP6_1317 Mcapitata_HTHC_TP6_1317 Mcapitata
## Mcapitata_HTHC_TP6_1604 Mcapitata_HTHC_TP6_1604 Mcapitata
## Mcapitata_HTHC_TP7_1126 Mcapitata_HTHC_TP7_1126 Mcapitata
## Mcapitata_HTHC_TP7_1250 Mcapitata_HTHC_TP7_1250 Mcapitata
## Mcapitata_HTHC_TP7_2419 Mcapitata_HTHC_TP7_2419 Mcapitata
## Mcapitata_HTHC_TP8_1082 Mcapitata_HTHC_TP8_1082 Mcapitata
## Mcapitata_HTHC_TP8_1246 Mcapitata_HTHC_TP8_1246 Mcapitata
## Mcapitata_HTHC_TP8_2067 Mcapitata_HTHC_TP8_2067 Mcapitata
## Mcapitata_HTHC_TP9_1078 Mcapitata_HTHC_TP9_1078 Mcapitata
## Mcapitata_HTHC_TP9_1331 Mcapitata_HTHC_TP9_1331 Mcapitata
## Mcapitata_HTHC_TP9_2009 Mcapitata_HTHC_TP9_2009 Mcapitata
## Mcapitata_HTHC_TP10_1074 Mcapitata_HTHC_TP10_1074 Mcapitata
## Mcapitata_HTHC_TP10_1332 Mcapitata_HTHC_TP10_1332 Mcapitata
## Mcapitata_HTHC_TP10_1689 Mcapitata_HTHC_TP10_1689 Mcapitata
## Mcapitata_HTHC_TP11_1178 Mcapitata_HTHC_TP11_1178 Mcapitata
## Mcapitata_HTHC_TP11_1270 Mcapitata_HTHC_TP11_1270 Mcapitata
## Mcapitata_HTHC_TP11_2511 Mcapitata_HTHC_TP11_2511 Mcapitata
## Mcapitata_HTHC_TP12_1140 Mcapitata_HTHC_TP12_1140 Mcapitata
## Mcapitata_HTHC_TP12_1274 Mcapitata_HTHC_TP12_1274 Mcapitata
## Mcapitata_HTHC_TP12_2190 Mcapitata_HTHC_TP12_2190 Mcapitata
## SRR5453739 SRR5453739 Mcapitata
## SRR5453740 SRR5453740 Mcapitata
## SRR5453741 SRR5453741 Mcapitata
## SRR5453742 SRR5453742 Mcapitata
## SRR5453743 SRR5453743 Mcapitata
## SRR5453744 SRR5453744 Mcapitata
## SRR5453745 SRR5453745 Mcapitata
## SRR5453746 SRR5453746 Mcapitata
## SRR5453747 SRR5453747 Mcapitata
## SRR5453748 SRR5453748 Mcapitata
## SRR5453749 SRR5453749 Mcapitata
## SRR5453750 SRR5453750 Mcapitata
## SRR5453751 SRR5453751 Mcapitata
## SRR5453752 SRR5453752 Mcapitata
## SRR5453753 SRR5453753 Mcapitata
## SRR5453754 SRR5453754 Mcapitata
## SRR5453755 SRR5453755 Mcapitata
## SRR5453756 SRR5453756 Mcapitata
## SRR5453757 SRR5453757 Mcapitata
## SRR5453758 SRR5453758 Mcapitata
## SRR5453759 SRR5453759 Mcapitata
## SRR5453760 SRR5453760 Mcapitata
## SRR5453761 SRR5453761 Mcapitata
## SRR5453762 SRR5453762 Mcapitata
## SRR5453763 SRR5453763 Mcapitata
## SRR5453764 SRR5453764 Mcapitata
## SRR5453765 SRR5453765 Mcapitata
## treatment timepoint
## Mcapitata_ATAC_TP11_2302 ATAC TP11
## Mcapitata_HTAC_TP11_2380 HTAC TP11
## Mcapitata_ATAC_TP6_2402 ATAC TP6
## Mcapitata_ATAC_TP12_2403 ATAC TP12
## Mcapitata_ATAC_TP1_1037 ATAC TP1
## Mcapitata_ATAC_TP1_1600 ATAC TP1
## Mcapitata_ATAC_TP1_1652 ATAC TP1
## Mcapitata_ATAC_TP3_1101 ATAC TP3
## Mcapitata_ATAC_TP3_1548 ATAC TP3
## Mcapitata_ATAC_TP3_1628 ATAC TP3
## Mcapitata_ATAC_TP4_1108 ATAC TP4
## Mcapitata_ATAC_TP4_1609 ATAC TP4
## Mcapitata_ATAC_TP4_1651 ATAC TP4
## Mcapitata_ATAC_TP5_1196 ATAC TP5
## Mcapitata_ATAC_TP5_1610 ATAC TP5
## Mcapitata_ATAC_TP5_1776 ATAC TP5
## Mcapitata_ATAC_TP6_1114 ATAC TP6
## Mcapitata_ATAC_TP6_1611 ATAC TP6
## Mcapitata_ATAC_TP7_1058 ATAC TP7
## Mcapitata_ATAC_TP7_1455 ATAC TP7
## Mcapitata_ATAC_TP7_1499 ATAC TP7
## Mcapitata_ATAC_TP8_1083 ATAC TP8
## Mcapitata_ATAC_TP8_1436 ATAC TP8
## Mcapitata_ATAC_TP8_1779 ATAC TP8
## Mcapitata_ATAC_TP9_1121 ATAC TP9
## Mcapitata_ATAC_TP9_1420 ATAC TP9
## Mcapitata_ATAC_TP9_1580 ATAC TP9
## Mcapitata_ATAC_TP10_1095 ATAC TP10
## Mcapitata_ATAC_TP10_1561 ATAC TP10
## Mcapitata_ATAC_TP10_1631 ATAC TP10
## Mcapitata_ATAC_TP11_1076 ATAC TP11
## Mcapitata_ATAC_TP11_1644 ATAC TP11
## Mcapitata_ATAC_TP12_1120 ATAC TP12
## Mcapitata_ATAC_TP12_1452 ATAC TP12
## Mcapitata_ATHC_TP1_1218 ATHC TP1
## Mcapitata_ATHC_TP1_1826 ATHC TP1
## Mcapitata_ATHC_TP1_2068 ATHC TP1
## Mcapitata_ATHC_TP3_1544 ATHC TP3
## Mcapitata_ATHC_TP3_2731 ATHC TP3
## Mcapitata_ATHC_TP3_2866 ATHC TP3
## Mcapitata_ATHC_TP4_1221 ATHC TP4
## Mcapitata_ATHC_TP4_2561 ATHC TP4
## Mcapitata_ATHC_TP4_2734 ATHC TP4
## Mcapitata_ATHC_TP5_1229 ATHC TP5
## Mcapitata_ATHC_TP5_1706 ATHC TP5
## Mcapitata_ATHC_TP5_2986 ATHC TP5
## Mcapitata_ATHC_TP6_1212 ATHC TP6
## Mcapitata_ATHC_TP6_2016 ATHC TP6
## Mcapitata_ATHC_TP6_2555 ATHC TP6
## Mcapitata_ATHC_TP7_1223 ATHC TP7
## Mcapitata_ATHC_TP7_2860 ATHC TP7
## Mcapitata_ATHC_TP7_2875 ATHC TP7
## Mcapitata_ATHC_TP8_1260 ATHC TP8
## Mcapitata_ATHC_TP8_2735 ATHC TP8
## Mcapitata_ATHC_TP8_2753 ATHC TP8
## Mcapitata_ATHC_TP9_1148 ATHC TP9
## Mcapitata_ATHC_TP9_2862 ATHC TP9
## Mcapitata_ATHC_TP9_2995 ATHC TP9
## Mcapitata_ATHC_TP10_1204 ATHC TP10
## Mcapitata_ATHC_TP10_2554 ATHC TP10
## Mcapitata_ATHC_TP10_2737 ATHC TP10
## Mcapitata_ATHC_TP11_1237 ATHC TP11
## Mcapitata_ATHC_TP11_2188 ATHC TP11
## Mcapitata_ATHC_TP11_2756 ATHC TP11
## Mcapitata_ATHC_TP12_1154 ATHC TP12
## Mcapitata_ATHC_TP12_2736 ATHC TP12
## Mcapitata_ATHC_TP12_2990 ATHC TP12
## Mcapitata_HTAC_TP1_1579 HTAC TP1
## Mcapitata_HTAC_TP1_2153 HTAC TP1
## Mcapitata_HTAC_TP1_2183 HTAC TP1
## Mcapitata_HTAC_TP3_1289 HTAC TP3
## Mcapitata_HTAC_TP3_1751 HTAC TP3
## Mcapitata_HTAC_TP3_2021 HTAC TP3
## Mcapitata_HTAC_TP4_1269 HTAC TP4
## Mcapitata_HTAC_TP4_1481 HTAC TP4
## Mcapitata_HTAC_TP4_2000 HTAC TP4
## Mcapitata_HTAC_TP5_1321 HTAC TP5
## Mcapitata_HTAC_TP5_1583 HTAC TP5
## Mcapitata_HTAC_TP5_1997 HTAC TP5
## Mcapitata_HTAC_TP6_1496 HTAC TP6
## Mcapitata_HTAC_TP6_1588 HTAC TP6
## Mcapitata_HTAC_TP6_1705 HTAC TP6
## Mcapitata_HTAC_TP7_1278 HTAC TP7
## Mcapitata_HTAC_TP7_1645 HTAC TP7
## Mcapitata_HTAC_TP7_1722 HTAC TP7
## Mcapitata_HTAC_TP8_1235 HTAC TP8
## Mcapitata_HTAC_TP8_2386 HTAC TP8
## Mcapitata_HTAC_TP8_2410 HTAC TP8
## Mcapitata_HTAC_TP9_1306 HTAC TP9
## Mcapitata_HTAC_TP9_1467 HTAC TP9
## Mcapitata_HTAC_TP9_2412 HTAC TP9
## Mcapitata_HTAC_TP10_1315 HTAC TP10
## Mcapitata_HTAC_TP10_1478 HTAC TP10
## Mcapitata_HTAC_TP10_1754 HTAC TP10
## Mcapitata_HTAC_TP11_1248 HTAC TP11
## Mcapitata_HTAC_TP11_1562 HTAC TP11
## Mcapitata_HTAC_TP12_1632 HTAC TP12
## Mcapitata_HTAC_TP12_1729 HTAC TP12
## Mcapitata_HTAC_TP12_2007 HTAC TP12
## Mcapitata_HTHC_TP1_1145 HTHC TP1
## Mcapitata_HTHC_TP1_1323 HTHC TP1
## Mcapitata_HTHC_TP1_2081 HTHC TP1
## Mcapitata_HTHC_TP3_1128 HTHC TP3
## Mcapitata_HTHC_TP3_1277 HTHC TP3
## Mcapitata_HTHC_TP3_2518 HTHC TP3
## Mcapitata_HTHC_TP4_1124 HTHC TP4
## Mcapitata_HTHC_TP4_1328 HTHC TP4
## Mcapitata_HTHC_TP4_2204 HTHC TP4
## Mcapitata_HTHC_TP5_1345 HTHC TP5
## Mcapitata_HTHC_TP5_1449 HTHC TP5
## Mcapitata_HTHC_TP5_1694 HTHC TP5
## Mcapitata_HTHC_TP6_1164 HTHC TP6
## Mcapitata_HTHC_TP6_1317 HTHC TP6
## Mcapitata_HTHC_TP6_1604 HTHC TP6
## Mcapitata_HTHC_TP7_1126 HTHC TP7
## Mcapitata_HTHC_TP7_1250 HTHC TP7
## Mcapitata_HTHC_TP7_2419 HTHC TP7
## Mcapitata_HTHC_TP8_1082 HTHC TP8
## Mcapitata_HTHC_TP8_1246 HTHC TP8
## Mcapitata_HTHC_TP8_2067 HTHC TP8
## Mcapitata_HTHC_TP9_1078 HTHC TP9
## Mcapitata_HTHC_TP9_1331 HTHC TP9
## Mcapitata_HTHC_TP9_2009 HTHC TP9
## Mcapitata_HTHC_TP10_1074 HTHC TP10
## Mcapitata_HTHC_TP10_1332 HTHC TP10
## Mcapitata_HTHC_TP10_1689 HTHC TP10
## Mcapitata_HTHC_TP11_1178 HTHC TP11
## Mcapitata_HTHC_TP11_1270 HTHC TP11
## Mcapitata_HTHC_TP11_2511 HTHC TP11
## Mcapitata_HTHC_TP12_1140 HTHC TP12
## Mcapitata_HTHC_TP12_1274 HTHC TP12
## Mcapitata_HTHC_TP12_2190 HTHC TP12
## SRR5453739 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453740 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453741 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453742 healthy_colony_healthy_tissue <NA>
## SRR5453743 healthy_colony_healthy_tissue <NA>
## SRR5453744 healthy_colony_healthy_tissue <NA>
## SRR5453745 growth_anomaly_colony_healthy_tissue <NA>
## SRR5453746 growth_anomaly_colony_healthy_tissue <NA>
## SRR5453747 growth_anomaly_colony_healthy_tissue <NA>
## SRR5453748 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453749 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453750 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453751 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453752 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453753 growth_anomaly_colony_growth_anomaly_tissue <NA>
## SRR5453754 healthy_colony_healthy_tissue <NA>
## SRR5453755 healthy_colony_healthy_tissue <NA>
## SRR5453756 healthy_colony_healthy_tissue <NA>
## SRR5453757 healthy_colony_healthy_tissue <NA>
## SRR5453758 healthy_colony_healthy_tissue <NA>
## SRR5453759 healthy_colony_healthy_tissue <NA>
## SRR5453760 growth_anomaly_colony_healthy_tissue <NA>
## SRR5453761 growth_anomaly_colony_healthy_tissue <NA>
## SRR5453762 growth_anomaly_colony_healthy_tissue <NA>
## SRR5453763 growth_anomaly_colony_healthy_tissue <NA>
## SRR5453764 growth_anomaly_colony_healthy_tissue <NA>
## SRR5453765 growth_anomaly_colony_healthy_tissue <NA>
## plugid reef reef_color ploidy
## Mcapitata_ATAC_TP11_2302 2302 Reef.18 #d8daeb 2
## Mcapitata_HTAC_TP11_2380 2380 Reef.18 #d8daeb 2
## Mcapitata_ATAC_TP6_2402 2402 Reef.18 #d8daeb 2
## Mcapitata_ATAC_TP12_2403 2403 Reef.18 #d8daeb 2
## Mcapitata_ATAC_TP1_1037 1037 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP1_1600 1600 Reef.42.43 #542788 2
## Mcapitata_ATAC_TP1_1652 1652 HIMB #b35806 2
## Mcapitata_ATAC_TP3_1101 1101 HIMB #b35806 2
## Mcapitata_ATAC_TP3_1548 1548 Reef.11.13 #fee0b6 2
## Mcapitata_ATAC_TP3_1628 1628 HIMB #b35806 2
## Mcapitata_ATAC_TP4_1108 1108 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP4_1609 1609 HIMB #b35806 2
## Mcapitata_ATAC_TP4_1651 1651 HIMB #b35806 2
## Mcapitata_ATAC_TP5_1196 1196 Reef.18 #d8daeb 2
## Mcapitata_ATAC_TP5_1610 1610 Reef.42.43 #542788 2
## Mcapitata_ATAC_TP5_1776 1776 Reef.42.43 #542788 2
## Mcapitata_ATAC_TP6_1114 1114 Reef.42.43 #542788 2
## Mcapitata_ATAC_TP6_1611 1611 Reef.42.43 #542788 2
## Mcapitata_ATAC_TP7_1058 1058 Lilipuna.Fringe #f1a340 2
## Mcapitata_ATAC_TP7_1455 1455 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP7_1499 1499 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP8_1083 1083 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP8_1436 1436 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP8_1779 1779 Reef.42.43 #542788 2
## Mcapitata_ATAC_TP9_1121 1121 HIMB #b35806 2
## Mcapitata_ATAC_TP9_1420 1420 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP9_1580 1580 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP10_1095 1095 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP10_1561 1561 Reef.11.13 #fee0b6 2
## Mcapitata_ATAC_TP10_1631 1631 HIMB #b35806 2
## Mcapitata_ATAC_TP11_1076 1076 Reef.35.36 #998ec3 2
## Mcapitata_ATAC_TP11_1644 1644 HIMB #b35806 2
## Mcapitata_ATAC_TP12_1120 1120 Reef.42.43 #542788 2
## Mcapitata_ATAC_TP12_1452 1452 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP1_1218 1218 Reef.11.13 #fee0b6 2
## Mcapitata_ATHC_TP1_1826 1826 Reef.11.13 #fee0b6 2
## Mcapitata_ATHC_TP1_2068 2068 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP3_1544 1544 Reef.18 #d8daeb 2
## Mcapitata_ATHC_TP3_2731 2731 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP3_2866 2866 HIMB #b35806 2
## Mcapitata_ATHC_TP4_1221 1221 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP4_2561 2561 Reef.18 #d8daeb 2
## Mcapitata_ATHC_TP4_2734 2734 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP5_1229 1229 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP5_1706 1706 Reef.11.13 #fee0b6 2
## Mcapitata_ATHC_TP5_2986 2986 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP6_1212 1212 Reef.11.13 #fee0b6 2
## Mcapitata_ATHC_TP6_2016 2016 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP6_2555 2555 Reef.18 #d8daeb 2
## Mcapitata_ATHC_TP7_1223 1223 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP7_2860 2860 HIMB #b35806 2
## Mcapitata_ATHC_TP7_2875 2875 HIMB #b35806 2
## Mcapitata_ATHC_TP8_1260 1260 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP8_2735 2735 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP8_2753 2753 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP9_1148 1148 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP9_2862 2862 HIMB #b35806 2
## Mcapitata_ATHC_TP9_2995 2995 Reef.11.13 #fee0b6 2
## Mcapitata_ATHC_TP10_1204 1204 Reef.11.13 #fee0b6 2
## Mcapitata_ATHC_TP10_2554 2554 Reef.18 #d8daeb 2
## Mcapitata_ATHC_TP10_2737 2737 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP11_1237 1237 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP11_2188 2188 Reef.35.36 #998ec3 2
## Mcapitata_ATHC_TP11_2756 2756 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP12_1154 1154 HIMB #b35806 2
## Mcapitata_ATHC_TP12_2736 2736 Reef.42.43 #542788 2
## Mcapitata_ATHC_TP12_2990 2990 Reef.18 #d8daeb 2
## Mcapitata_HTAC_TP1_1579 1579 Lilipuna.Fringe #f1a340 2
## Mcapitata_HTAC_TP1_2153 2153 Reef.18 #d8daeb 2
## Mcapitata_HTAC_TP1_2183 2183 Reef.42.43 #542788 2
## Mcapitata_HTAC_TP3_1289 1289 Reef.35.36 #998ec3 2
## Mcapitata_HTAC_TP3_1751 1751 Reef.42.43 #542788 2
## Mcapitata_HTAC_TP3_2021 2021 Reef.42.43 #542788 2
## Mcapitata_HTAC_TP4_1269 1269 Reef.35.36 #998ec3 2
## Mcapitata_HTAC_TP4_1481 1481 Reef.35.36 #998ec3 2
## Mcapitata_HTAC_TP4_2000 2000 HIMB #b35806 2
## Mcapitata_HTAC_TP5_1321 1321 Reef.11.13 #fee0b6 2
## Mcapitata_HTAC_TP5_1583 1583 Lilipuna.Fringe #f1a340 2
## Mcapitata_HTAC_TP5_1997 1997 HIMB #b35806 2
## Mcapitata_HTAC_TP6_1496 1496 Reef.35.36 #998ec3 2
## Mcapitata_HTAC_TP6_1588 1588 Reef.18 #d8daeb 2
## Mcapitata_HTAC_TP6_1705 1705 Reef.35.36 #998ec3 2
## Mcapitata_HTAC_TP7_1278 1278 Reef.11.13 #fee0b6 2
## Mcapitata_HTAC_TP7_1645 1645 Reef.42.43 #542788 2
## Mcapitata_HTAC_TP7_1722 1722 Reef.35.36 #998ec3 2
## Mcapitata_HTAC_TP8_1235 1235 Reef.42.43 #542788 2
## Mcapitata_HTAC_TP8_2386 2386 Reef.18 #d8daeb 2
## Mcapitata_HTAC_TP8_2410 2410 Reef.18 #d8daeb 2
## Mcapitata_HTAC_TP9_1306 1306 Lilipuna.Fringe #f1a340 2
## Mcapitata_HTAC_TP9_1467 1467 Reef.11.13 #fee0b6 2
## Mcapitata_HTAC_TP9_2412 2412 Reef.18 #d8daeb 2
## Mcapitata_HTAC_TP10_1315 1315 Lilipuna.Fringe #f1a340 2
## Mcapitata_HTAC_TP10_1478 1478 Reef.11.13 #fee0b6 2
## Mcapitata_HTAC_TP10_1754 1754 HIMB #b35806 2
## Mcapitata_HTAC_TP11_1248 1248 HIMB #b35806 2
## Mcapitata_HTAC_TP11_1562 1562 Reef.11.13 #fee0b6 2
## Mcapitata_HTAC_TP12_1632 1632 HIMB #b35806 4
## Mcapitata_HTAC_TP12_1729 1729 Reef.18 #d8daeb 2
## Mcapitata_HTAC_TP12_2007 2007 Reef.42.43 #542788 2
## Mcapitata_HTHC_TP1_1145 1145 HIMB #b35806 2
## Mcapitata_HTHC_TP1_1323 1323 Reef.35.36 #998ec3 2
## Mcapitata_HTHC_TP1_2081 2081 HIMB #b35806 2
## Mcapitata_HTHC_TP3_1128 1128 HIMB #b35806 2
## Mcapitata_HTHC_TP3_1277 1277 HIMB #b35806 2
## Mcapitata_HTHC_TP3_2518 2518 Reef.18 #d8daeb 2
## Mcapitata_HTHC_TP4_1124 1124 Reef.42.43 #542788 2
## Mcapitata_HTHC_TP4_1328 1328 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP4_2204 2204 Reef.42.43 #542788 2
## Mcapitata_HTHC_TP5_1345 1345 Reef.18 #d8daeb 2
## Mcapitata_HTHC_TP5_1449 1449 Lilipuna.Fringe #f1a340 2
## Mcapitata_HTHC_TP5_1694 1694 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP6_1164 1164 Reef.35.36 #998ec3 2
## Mcapitata_HTHC_TP6_1317 1317 Reef.35.36 #998ec3 2
## Mcapitata_HTHC_TP6_1604 1604 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP7_1126 1126 Reef.42.43 #542788 2
## Mcapitata_HTHC_TP7_1250 1250 Reef.42.43 #542788 2
## Mcapitata_HTHC_TP7_2419 2419 Reef.18 #d8daeb 2
## Mcapitata_HTHC_TP8_1082 1082 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP8_1246 1246 Reef.42.43 #542788 2
## Mcapitata_HTHC_TP8_2067 2067 HIMB #b35806 2
## Mcapitata_HTHC_TP9_1078 1078 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP9_1331 1331 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP9_2009 2009 Lilipuna.Fringe #f1a340 2
## Mcapitata_HTHC_TP10_1074 1074 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP10_1332 1332 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP10_1689 1689 Reef.11.13 #fee0b6 2
## Mcapitata_HTHC_TP11_1178 1178 Lilipuna.Fringe #f1a340 2
## Mcapitata_HTHC_TP11_1270 1270 HIMB #b35806 2
## Mcapitata_HTHC_TP11_2511 2511 Reef.18 #d8daeb 2
## Mcapitata_HTHC_TP12_1140 1140 HIMB #b35806 2
## Mcapitata_HTHC_TP12_1274 1274 HIMB #b35806 2
## Mcapitata_HTHC_TP12_2190 2190 Reef.42.43 #542788 2
## SRR5453739 Mcap_KA2 Kiholo #33a02c 2
## SRR5453740 Mcap_KA3 Kiholo #33a02c 2
## SRR5453741 Mcap_KA5 Kiholo #33a02c 2
## SRR5453742 Mcap_KH1 Kiholo #33a02c 2
## SRR5453743 Mcap_KH2 Kiholo #33a02c 2
## SRR5453744 Mcap_KH8 Kiholo #33a02c 2
## SRR5453745 Mcap_KU2 Kiholo #33a02c 2
## SRR5453746 Mcap_KU3 Kiholo #33a02c 2
## SRR5453747 Mcap_KU5 Kiholo #33a02c 2
## SRR5453748 Mcap_WA8 Waiopae #1f78b4 2
## SRR5453749 Mcap_WA1 Waiopae #1f78b4 2
## SRR5453750 Mcap_WA2 Waiopae #1f78b4 2
## SRR5453751 Mcap_WA12 Waiopae #1f78b4 2
## SRR5453752 Mcap_WA3 Waiopae #1f78b4 2
## SRR5453753 Mcap_WA5 Waiopae #1f78b4 2
## SRR5453754 Mcap_WH3 Waiopae #1f78b4 2
## SRR5453755 Mcap_WH8 Waiopae #1f78b4 2
## SRR5453756 Mcap_WH1 Waiopae #1f78b4 2
## SRR5453757 Mcap_WH5 Waiopae #1f78b4 2
## SRR5453758 Mcap_WH2 Waiopae #1f78b4 2
## SRR5453759 Mcap_WH12 Waiopae #1f78b4 2
## SRR5453760 Mcap_WU8 Waiopae #1f78b4 2
## SRR5453761 Mcap_WU1 Waiopae #1f78b4 2
## SRR5453762 Mcap_WU2 Waiopae #1f78b4 2
## SRR5453763 Mcap_WU12 Waiopae #1f78b4 2
## SRR5453764 Mcap_WU3 Waiopae #1f78b4 2
## SRR5453765 Mcap_WU5 Waiopae #1f78b4 2
## ploidy_color group group_color
## Mcapitata_ATAC_TP11_2302 #01665e Group1 #1f78b4
## Mcapitata_HTAC_TP11_2380 #01665e Group1 #1f78b4
## Mcapitata_ATAC_TP6_2402 #01665e Group2 #33a02c
## Mcapitata_ATAC_TP12_2403 #01665e Group2 #33a02c
## Mcapitata_ATAC_TP1_1037 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP1_1600 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP1_1652 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP3_1101 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP3_1548 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP3_1628 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP4_1108 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP4_1609 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP4_1651 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP5_1196 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP5_1610 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP5_1776 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP6_1114 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP6_1611 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP7_1058 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP7_1455 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP7_1499 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP8_1083 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP8_1436 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP8_1779 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP9_1121 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP9_1420 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP9_1580 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP10_1095 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP10_1561 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP10_1631 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP11_1076 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP11_1644 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP12_1120 #01665e Ungrouped #808080
## Mcapitata_ATAC_TP12_1452 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP1_1218 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP1_1826 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP1_2068 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP3_1544 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP3_2731 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP3_2866 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP4_1221 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP4_2561 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP4_2734 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP5_1229 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP5_1706 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP5_2986 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP6_1212 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP6_2016 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP6_2555 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP7_1223 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP7_2860 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP7_2875 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP8_1260 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP8_2735 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP8_2753 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP9_1148 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP9_2862 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP9_2995 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP10_1204 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP10_2554 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP10_2737 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP11_1237 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP11_2188 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP11_2756 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP12_1154 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP12_2736 #01665e Ungrouped #808080
## Mcapitata_ATHC_TP12_2990 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP1_1579 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP1_2153 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP1_2183 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP3_1289 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP3_1751 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP3_2021 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP4_1269 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP4_1481 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP4_2000 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP5_1321 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP5_1583 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP5_1997 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP6_1496 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP6_1588 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP6_1705 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP7_1278 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP7_1645 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP7_1722 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP8_1235 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP8_2386 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP8_2410 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP9_1306 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP9_1467 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP9_2412 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP10_1315 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP10_1478 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP10_1754 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP11_1248 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP11_1562 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP12_1632 #7570b3 Ungrouped #808080
## Mcapitata_HTAC_TP12_1729 #01665e Ungrouped #808080
## Mcapitata_HTAC_TP12_2007 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP1_1145 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP1_1323 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP1_2081 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP3_1128 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP3_1277 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP3_2518 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP4_1124 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP4_1328 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP4_2204 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP5_1345 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP5_1449 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP5_1694 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP6_1164 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP6_1317 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP6_1604 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP7_1126 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP7_1250 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP7_2419 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP8_1082 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP8_1246 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP8_2067 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP9_1078 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP9_1331 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP9_2009 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP10_1074 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP10_1332 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP10_1689 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP11_1178 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP11_1270 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP11_2511 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP12_1140 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP12_1274 #01665e Ungrouped #808080
## Mcapitata_HTHC_TP12_2190 #01665e Ungrouped #808080
## SRR5453739 #01665e SRA-Kiholo #543005
## SRR5453740 #01665e SRA-Kiholo #543005
## SRR5453741 #01665e SRA-Kiholo #543005
## SRR5453742 #01665e SRA-Kiholo #543005
## SRR5453743 #01665e SRA-Kiholo #543005
## SRR5453744 #01665e SRA-Kiholo #543005
## SRR5453745 #01665e SRA-Kiholo #543005
## SRR5453746 #01665e SRA-Kiholo #543005
## SRR5453747 #01665e SRA-Kiholo #543005
## SRR5453748 #01665e SRA-Waiopae #dfc27d
## SRR5453749 #01665e SRA-Waiopae #dfc27d
## SRR5453750 #01665e SRA-Waiopae #dfc27d
## SRR5453751 #01665e SRA-Waiopae #dfc27d
## SRR5453752 #01665e SRA-Waiopae #dfc27d
## SRR5453753 #01665e SRA-Waiopae #dfc27d
## SRR5453754 #01665e SRA-Waiopae #dfc27d
## SRR5453755 #01665e SRA-Waiopae #dfc27d
## SRR5453756 #01665e SRA-Waiopae #dfc27d
## SRR5453757 #01665e SRA-Waiopae #dfc27d
## SRR5453758 #01665e SRA-Waiopae #dfc27d
## SRR5453759 #01665e SRA-Waiopae #dfc27d
## SRR5453760 #01665e SRA-Waiopae #dfc27d
## SRR5453761 #01665e SRA-Waiopae #dfc27d
## SRR5453762 #01665e SRA-Waiopae #dfc27d
## SRR5453763 #01665e SRA-Waiopae #dfc27d
## SRR5453764 #01665e SRA-Waiopae #dfc27d
## SRR5453765 #01665e SRA-Waiopae #dfc27d
Load pairwise percent shared SNP results and convert if from one line per pair format into a symetric matrix uisng the xtabs function.
pairwise_percent_shared <- read.table("GVCFall.filtered.recode.vcf.gz.allelic_similarity.full.tsv", sep='\t', header=T)
pairwise_percent_shared.matrix <- xtabs(match_perc ~ ind1 + ind2, data=pairwise_percent_shared)
Process the simScore data ready for plotting (i.e., cluster samples based on computed distance and construct a dendrogram of the relationship).
# Make a copy of input matrix
tmp.mat <- pairwise_percent_shared.matrix
# Generate clusters from the allelic similarity scores matrix
tmp.mat.dist <- dist(tmp.mat, method="euclidean")
tmp.mat.hclust <- hclust(tmp.mat.dist, method="complete")
# Get sample colors for sidebar in the same order as the matrix
Rcols <- samples.info[rownames(tmp.mat),]$group_color
Ccols <- samples.info[colnames(tmp.mat),]$group_color
# Get min and max values of matrix
tmp.mat.min <- min(tmp.mat); tmp.mat.min
## [1] 77.95
tmp.mat.max <- max(tmp.mat); tmp.mat.max
## [1] 100
Plot clustering results and write dendrogram to file.
simScore.dendro <- as.dendrogram(tmp.mat.hclust)
write.dendrogram(simScore.dendro, "cluster_dendrogram.tre", edges=TRUE)
plot(tmp.mat.hclust)
Write ordered matrix to file incase we want it later.
tmp.mat.order <- dendro_data(simScore.dendro, type="rectangle")[["labels"]][["label"]]
tmp.mat.ordered <- tmp.mat[
order(match(rownames(tmp.mat), rev(tmp.mat.order))),
order(match(colnames(tmp.mat), tmp.mat.order))
]
write.table(as.matrix(tmp.mat.ordered),
"GVCFall.filtered.recode.vcf.gz.allelic_similarity.full.matrix.tsv",
sep='\t', quote=FALSE,
row.names=TRUE, col.names=TRUE)
Plot simScores heatmap.
par(cex.main=0.7, cex.lab=0.9, cex.axis=0.9) # Change the font size of the legend title, labels and axis
heatmap.2(x=tmp.mat,
Rowv = simScore.dendro,
Colv = simScore.dendro,
col=cividis(length(seq(75, 100, 0.1))-1),
breaks=seq(75, 100, 0.1),
trace="none", # Dont draw "trace" line
key=TRUE, # Show color-key
margins=c(8,8), # Numeric vector of length 2 containing the margins for column and row names, respectively.
ColSideColors=Ccols,
RowSideColors=Rcols,
offsetRow=0,
offsetCol=0,
cexRow=cexSize, # Positive numbers, used as cex.axis in for the row or column axis labeling.
cexCol=cexSize,
cellnote=formatC(tmp.mat, big.mark=","),
notecex=0.1,
)